Extended Data Fig. 7: Clustering and cell-type assignment analysis of all cells from 20 developmental stages of zebrafish embryogenesis.

a-c, UMAP visualization and clustering analysis of all cells from 20 developmental stages of zebrafish embryogenesis without experimental batch-effect correction, colored by 36 broad cell types (a), stages (b), and experimental batches (c). The colors of 36 broad cell types in Extended Data Fig. 7a are the same as in Fig. 3b. d, UMAP visualization of all cells from 20 developmental stages of zebrafish embryogenesis with experimental batch-effect correction by ArchR, colored by experimental batches. e-h, UMAP visualization of all cells from 20 developmental stages of zebrafish embryogenesis with experimental batch-effect correction by ArchR and Harmony, colored by doublets enrichment score (e), the fraction of fragment in peaks (f), unique fragment number (g), and TSS enrichment score (h) of each cell. i, UMAP projection of all cells colored by gene activity scores reflecting accessibility within several selected cell lineage marker genes.